search

ecohealthalliance / diagnostic-dashboard

GRITS uses natural language processing to extract disease-related information from text, including disease names, symptoms, dates, locations, case and death counts, and more.
http://grits.eha.io
Apache License 2.0
6 stars 0 forks source link

readme

GRITS Diagnostic Dashboard

The diagnostic dashboard provides the web-based user interface for the GRITS system. Here users can create accounts and log in, view their usage history, submit new articles for processing, and view the complete results of processing an article. The output of processing includes extracted features such as locations, dates, symptoms, case counts, a timeline, visualizations, and the differential diagnosis for diseases inferred from the article.

Dependencies

The diagnostic dashboard is a meteor application. It uses several meteor plugins which may be installed using the instructions and scripts detailed below.

The dashboard relies on a Python backend whose code is available in the grits-api project.

Diagnostic Dashboard set-up

As part of total GRITS deployment

You may elect to install all GRITS components at once by following the instructions in the grits-deploy-scripts grits-deploy-ansible project.

Config for quick deploy and quick install

Create a new config file that sets the variables from config.sample:

$ cp config.sample config

and edit the values to suit your environment.

Quick deploy

If you've done this before and have a server instance ready to go with diagnostic-dashboard in your home, and you have your config file set up, use the shorthand method:

  $ ssh -i key.pem ubuntu@instance GIT_USER=user GIT_PASSWORD=password 'bash -s' < install.sh

Quick install

If you already have the codebase and have set up your config file, simply run install.sh from the project directory:

  $ sh install.sh

Note this script assumes your diagnostic-dashboard directory is in your home; edit to suit. It also requires that you have an environment variable named APACHE_URL set to the root URL of your server, e.g.:

  $ export APACHE_URL=http://localhost

or

  $ export APACHE_URL=http://my-server.com

This will install meteor, meteorite and forever. It then will run deploy.sh which will update the Meteor package dependencies, create a bundle of the app, and begin running the server.

The service will start on port 3001: http://localhost:3001/profile

Functionality will be very limited without a correpondsing grits-api backend, so make sure to install that project as well.

Detailed setup

Clone this repository if you don't already have a local copy:

$ git clone git@github.com:ecohealthalliance/diagnostic-dashboard.git

If you wish to install all dependencies, bundle the app, and begin running it immediately, simply execute the install.sh script, which in turn invokes deploy.sh as described above:

$ sh install.sh

Otherwise, you may complete the following steps and omit any that may not be necessary for you.

If for example you already have Meteor >= 0.8 installed, you can omit the followng step:

$ curl https://install.meteor.com/ | sh

Install npm if necessary:

$ curl http://npmjs.org/install.sh | sh

mInstall meteorite and forever, globally:

$ sudo npm install -g meteorite forever

Change directory to wherever you've put the diagnostic-dashboard repository:

$ cd ~/diagnostic-dashboard

Update the meteorite dependencies:

$ mrt update

Start the service:

$ meteor

The service will start on port 3000: http://localhost:3000/profile

Before you can use the most interesting parts of the GRITS application, you'll need to make sure your diagnostic-dashboard server has access to its corresponding backend API server, so consult the documentation in the grits-api project and install that as well.

Full local setup

The following are all the commands needed for a local setup.

git clone git@github.com:ecohealthalliance/diagnostic-dashboard.git
cd diagnostic-dashboard
cp config.sample config
export APACHE_URL=http://localhost
curl https://install.meteor.com/ | sh
curl http://npmjs.org/install.sh | sh
sudo rm -rf ~/tmp
sudo rm -rf ~/.npm
sudo npm install -g meteorite forever
mrt update
meteor

License

Copyright 2016 EcoHealth Alliance

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.